User:Eric Martz/Sandbox 13

Sequence Alignment Tools

What I want:
 * 1) % identity vs. length of each chain and number of identical residues/chain length for each chain
 * 2) colors that indicate identity/similarity/difference
 * 3) ability to block a region of the alignment and get identity and length for that region (could cut and paste a new job ...)

Uniprot.org

 * no % ident
 * gray colors

Jalview
Seems to be mostly an alignment editing tool.

ClustalW2 at EBI
ClustalW2
 * has colors but no color key
 * no % id (?!)
 * give a score but doesn't explain it.

RCSB Compare Structures

 * Smith-Waterman or Needleman-Wunsch does #1,#2 but only for sequences of 3D structures.
 * Smith-Waterman shows only the aligned segments, while Needleman-Wunsch shows full length with gaps.

Swiss-Model
Why doesn't it make a model of FlgE CamJe using 1wlg?

>tr|Q83WM5|Q83WM5_CAMJE FlgE OS=Campylobacter jejuni GN=flgE PE=4 SV=1 MMRSLWSGVSGLQAHQVAMDVEGNNISNVNTTGFKYSRADFGTMFSQTVKIATAPTDGRG GSNPLQIGLGVSVSSTTRIHSQGSVQTTDKNTDVAINGDGFFMVSDDGGLTRYLTRSGDF KLDAYGNFVNNAGFVVQGWNINWDTQSIDSSRTPQNIFIDPGMHIPAAKSTEVAIKANLN SGLSVGTAKTPIYGLDSVHGFNKKDGTAKNENDTGITQFYTTSKNSVEVTEKGVDCAALF NGKGDGLNLRDGQGIWVSYADSKFSTDVPNGVNVFNPNTQATQNGVIFWGDENNAVNLDI TLNGVRIQNNSIKSLDQAIEYINTFTAPTDTREGTGVKAVRKADGSGIEFINTNADGTTD NMKNIDLVVNQANTAGERHNLTWQANNNSFQATSRKQGANSVWIPGNNPVNGTERIQIVT AHKYVYSSTPVQLDPMYNPDGGPAFNQANINTPGTAENNYRNAVNGSLLNTTVRTFRTTE DLRELLQRDARYGVDYDGSGGFEADGSDVNEGVKVTVGATGEFIISNPNVQSTPPNGIVQ NNRRPHDISFNVTAYTDAKGKVSTNMAFTNIFKGFDGVLTVGNSNRQSEQLFLSAFSAGL EIYDSLGSKHTLEVQFVKQSTTQDGGNEWQMIIRVPEPAEINTTGEGPNNIIVGTARFNN DGSLANYSPKTINFSPNNGAAPNQQIKLSFGTSGSNDGLVSSNSASTLTGQATDGYTSGN LKPDAIRVDDKGNILGEFTNGKTFAVAKMAMASVANNSGLEEIGGNLFKVTANSGAIVVG EAGTGGRGEMKTSALEMSNVDLSRSLTELIIIQRGYQANSKTISTSDQMLQTLIQLKQ >sp|P0A1J1|FLGE_SALTY Flagellar hook protein flgE OS=Salmonella typhimurium GN=flgE PE=1 SV=2 MSFSQAVSGLNAAATNLDVIGNNIANSATYGFKSGTASFADMFAGSKVGLGVKVAGITQD FTDGTTTNTGRGLDVAISQNGFFRLVDSNGSVFYSRNGQFKLDENRNLVNMQGMQLTGYP ATGTPPTIQQGANPAPITIPNTLMAAKSTTTASMQINLNSTDPVPSKTPFSVSDADSYNK KGTVTVYDSQGNAHDMNVYFVKTKDNEWAVYTHDSSDPAATAPTTASTTLKFNENGILES GGTVNITTGTINGATAATFSLSFLNSMQQNTGANNIVATNQNGYKPGDLVSYQINNDGTV VGNYSNEQEQVLGQIVLANFANNEGLASQGDNVWAATQASGVALLGTAGSGNFGKLTNGA LEASNVDLSKELVNMIVAQRNYQSNAQTIKTQDQILNTLVNLR